Ethnic Khoisans (also sometimes called San, !Kung, or Bushmen, terms that heavily overlap but do not mean quite the same thing), are associated one of the main hunter-gatherer societies of Africa from the most ancient times (ethnic Pygmies are associated with the other main hunter-gatherer society of Africa from the most ancient times). This theory is supported by their genetic diversity:
Analyses of the men’s genomes confirm that the Bushmen, also known as San or Khoisan, are among the most genetically diverse people in the world. Two Bushmen who live within walking distance of each other might have more genetic differences between them than a European and an Asian.
Genetic diversity as a sign of a historically ancient gene pool is the flip side of the "founder effect" that leads small groups that broke away from a larger population and then expanded in population to have low genetic diversity.
The Khoisan's level of genetic diversity suggests that diverged from their fellow modern humans who migrated out of Africa around 100,000 years ago, and are likewise relatively distant relatives of other African populations (based on incomplete genome typing done to date). Khoisan populations are as distinct from Africans of Niger-Congo ethnicity (which includes Congo) as they are from Europeans.
Genetic evidence clearly puts Khoisan's in a distinct genetic cluster from Bantu and Yoruba populations (which are also clearly distinct from each other), and each of the African populations have much more genetic diversity than the people of Europe do.
The Bantu ethnicity is associated with the West African civilization that was the first in Africa to develop agriculture than then rapidly expand across a large swath of the continent (in the time period from about 1500 BC to 1000 AD), mostly by replacing or displacing prior populations. This expansion was relatively recent in historic terms when it reached its furthest extent in Southern Africa at the time that Europeans first arrived on the contingent. Linguistic evidence (the great similarity between Bantu languages) corroborates this link and helps fix the suspected point of origin for the Bantus to a very specific geographic location. Comparable expansions in Europe and China took place many millenia earlier.
Prior to Bantu expansion, the Khoisans are believed to have been the predominant ethnic group in Southern Africa and up into parts of East Africa. Linguistically, Khoisan languages are distinguished by their use of clicks as phonemes. Now, Khoisans are a small minority in Southern Africa which is predominant mostly in and around the Kalahari desert.
According to the earlier mtDNA study cited above, estimates that a common point of origin of "all African mtDNAs, of 125,500–165,500 years before the present, a date that is concordant with all previous estimates derived from mtDNA and other genetic data, for the time of origin of modern humans in Africa."
A couple other footnotes to the research are worth noting:
Until now, only one African genome – the genetic makeup of a person from the [predominantly Nigerian] Yoruba ethnic group – had been completed. . . .
The new research also reveals evidence of mixture between hunter-gatherer Bushmen and agricultural Bantu people. Tutu has a female heritage marker usually found only in Bushmen, indicating that the archbishop had a female Bushman ancestor. And one of the Bushmen has a type of Y chromosome often found in Bantu men, indicating a Bantu male ancestor.
One of the reasons it was scientifically important to secure Khoisan genomes now is that there is a good chance that there will be very "pure blooded" or near "pure blooded" Khoisan's in a few generations because they are such a small minority population in Africa and hunter-gatherer societies do not have a good track record in modern times. Without this information, one side of the arguably oldest split in the modern human genetic heritage might be lost forever.
I am interested in the nature of the interaction between (1) various Bantu-speaking colonists, and (2) European colonists, with the autochthones (Khoisan) in South Africa. Have any studies been done comparing data from Mitochondrial DNA with Y-DNA? The significance of this would be to identify differences between forced and transactional concubinage, which would in turn tell us about different colonising strategies.
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